CINXE.COM
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
<html> <head> <title> Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor </title> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="icon" href="/static/favicon.ico" type="image/x-icon"/> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" id="MathJax-script"></script> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script> <link disabled rel="stylesheet" href="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/styles/default.min.css"> <script async src="//cdn.jsdelivr.net/gh/highlightjs/cdn-release@9.18.0/build/highlight.min.js"></script> <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-55275703-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag() { dataLayer.push(arguments); } gtag('js', new Date()); gtag('config', "UA-55275703-1"); </script> <link rel="stylesheet" href="/static/CACHE/css/output.b3e21268cb4d.css" type="text/css"> <script src="/static/CACHE/js/output.8d9edd4e014b.js"></script> <link rel="stylesheet" href="/static/autocomplete/tribute.css" /> <link rel="stylesheet" href="/static/autocomplete/at.who.css" /> <link href="/static/pagedown.css" type="text/css" media="all" rel="stylesheet"> <link href="/static/prism.css" rel="stylesheet"> <link href="/static/pagedown/demo/browser/demo.css" type="text/css" media="all" rel="stylesheet"> <script src="/static/autocomplete/tribute.js"></script> <script type="text/javascript" src="/static/pagedown/Markdown.Converter.js"></script> <script type="text/javascript" src="/static/pagedown-extra/pagedown/Markdown.Converter.js"></script> <script type="text/javascript" src="/static/pagedown/Markdown.Sanitizer.js"></script> <script type="text/javascript" src="/static/pagedown/Markdown.Editor.js"></script> <script type="text/javascript" src="/static/pagedown-extra/Markdown.Extra.js"></script> <script type="text/javascript" src="/static/pagedown_init.js"></script> <script src="/static/prism.js"></script> <script src="/static/markdown-it.js"></script> <script src="/static/autocomplete/at.who.js"></script> </head> <body itemscope itemtype="https://schema.org/QAPage"> <div class="ui inverted container main"> <span class="menus"> <div class="ui top attached text menu" id="menu-topics"> <div class="ui inverted dimmer"></div> <div class="right menu" id="login-opts"> <a class="item " href="/accounts/login/"> <i class="sign-in icon"></i>Log In</a> <a class="item " href="/accounts/signup/"> <i class="user icon"></i> Sign Up</a> <a class="item " href="/info/about/"> <i class="info icon"></i>about</a> <a class="item " href="/info/faq/"> <i class="question icon"></i> faq </a> </div> </div> <div class="ui labeled icon attached pointing menu" id="menu-header"> <div class="header item" id="logo"> <a href="https://support.bioconductor.org/"><img class="ui image" src="/static/transparent-logo.png"></a> </div> <a class="item format add-question" href="/new/post/"> <span class="">Ask a question</span> </a> <a class="item format " href="/"> <span class="">Latest</span> </a> <a class=" item format" href="/t/news/"> <span class="">News</span> </a> <a class=" item format " href="/t/jobs/"> <span class="">Jobs</span> </a> <a class=" item format " href="/t/tutorials/"> <span class="">Tutorials</span> </a> <a class=" item format " href="/t/"> <span class="">Tags</span> </a> <a class=" item format " href="/user/list/"> <span class="">Users</span> </a> </div> </span> <span class="phone-menus"> <div class="header item" id="logo"> <a href="/"><img class="ui image" width="220px" src="/static/transparent-logo.png"></a> </div> <div class="ui labeled icon attached fluid pointing menu" id="menu-header" style="background-color: white"> <div class="ui left simple dropdown item"> <i class="bars icon"><i class="dropdown icon"></i></i> <div class="menu"> <a class="item " href="/new/post/"> <i class=" edit icon"></i>New Post </a> <a class="item " href="/"> <i class=" list icon"></i> Latest </a> <a class="item " href="/t/news/"> <i class=" newspaper icon"></i> News </a> <a class="item " href="/t/jobs/"> <i class=" briefcase icon"></i> Jobs </a> <a class="item " href="/t/tutorials/"> <i class=" info circle icon"></i> Tutorials </a> <a class="item " href="/t/"> <i class="tag icon"></i>Tags </a> <a class="item " href="/user/list/"> <i class=" world icon"></i> Users </a> </div> </div> <div class="ui right simple dropdown item"> </div> <div class="ui right simple dropdown item"> <i class="user icon"><i class="dropdown icon"></i></i> <div class="menu" id="login-opts"> <a class="item " href="/accounts/login/"><i class="sign-in icon"></i> Log In</a> <a class="item " href="/accounts/signup/"><i class="arrow circle up icon"></i> Sign Up</a> <a class="item " href="/info/about/"><i class="info circle icon"></i>About </a> </div> </div> </div> </span> <div class="ui bottom attached segment block"> <div class="ui stackable grid"> <div class="fit twelve wide content column"> <span itemprop="mainEntity" itemscope itemtype="https://schema.org/Question"> <div class="ui vertical segment"> <a name="80845"></a> <div class="post view open" data-value="80845"> <div class="title" itemprop="name">Tutorial:Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor</div> <span itemprop="answerCount" style="display: none">0</span> <div class="body" > <div class="voting"> <button class="ui icon button" data-value="upvote" data-state="0"><i class="thumbs up icon"></i> </button> <div class="score" itemprop="upvoteCount">5</div> <button class="ui icon button" data-value="bookmark" data-state="0"><i class="bookmark icon"></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="wrap magnify"> <div class="user_box tablet right"> <div> <a class="" href="/u/8324/"> <img class="ui centered circular image" src="https://secure.gravatar.com/avatar/5ceb6894a7d0cd33ab2f2c9b1b50c272?s=80&d=identicon"> </a> </div> <div class="muted"> <div><a href="/u/8324/">phil.chapman</a> ▴ 150 </div> @philchapman-8324 <div>Last seen 8.2 years ago</div> <div>United Kingdom</div> </div> </div> <span itemprop="text"> <p>We've just been trialling the <a rel="nofollow" href="http://www.nature.com/nmeth/journal/v11/n12/full/nmeth.f.376.html">Lexogen Quantseq 3'-UTR RNAseq protocol </a>and I thought I'd share the write-up I put together in case anyone else finds it useful.聽 I really valued being able to do this all in Bioconductor since I wasn't having to swap environments all the time to use different tools and work out what was going on.聽 The techniques used include:</p> <ul> <li>ShortRead to manipulate, filter and quality check reads</li> <li>RSubread to do the alignment</li> <li>RSubread to do the feature counting</li> <li>ensembldb to conveniently access annotation</li> <li>ggplot2 and the cowplot extension for doing nice plots</li> </ul> <p><a rel="nofollow" href="http://rpubs.com/chapmandu2/171024">http://rpubs.com/chapmandu2/171024</a></p> <p>Thanks also to Martin for help with ShortRead.</p> <p>聽</p> <p>聽</p> </span> </div> <span class="inplace-tags"> <a class="ptag" href="/tag/shortread/"> shortread </a> <a class="ptag" href="/tag/rsubread/"> rsubread </a> <a class="ptag" href="/tag/ensembldb/"> ensembldb </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> • 3.5k views </span> <time itemprop="dateCreated" datetime="2016-04-14"></time> <div class="actions top-level"> <a class="add-comment ui tiny label">ADD COMMENT</a> • <a itemprop="url" href="/p/80845/#80845">link</a> <span class="status muted user-info"> <span> 8.6 years ago <a href="/u/8324/"> phil.chapman </a> ▴ 150 </span> </span> </div> <span class="diff-cont"></span> </div> <div class="comment-list"> <div class="indent" ><div> <a name="101846"></a> <div class="post comment open" data-value="101846"> <div class="body"> <div class="voting"> <button class="ui icon mini button" data-value="upvote" data-state="0"> <i class="thumbs up icon "></i> </button> <div class="score">0</div> <button class="ui icon mini button bookmark" data-value="bookmark" data-state="0"> <i class="bookmark icon "></i> </button> </div> <div class="content"> <div class="droppable inplace"> <div class="ui inverted dimmer"> <div class="ui text loader"> <div class="muted">Entering edit mode</div> </div> </div> <div class="magnify"> <p>Thanks a lot for sharing your workflow!</p> <p>Just curious: the titles says "<em>Analysis of Lexogen Quantseq Data: <strong>Part 1</strong></em>". Is there a "Part 2" anywhere?</p> </div> <div class="actions "> <a class="add-comment ui tiny label">ADD REPLY</a> • <a itemprop="url" href="/p/80845/#101846">link</a> <span class="status muted user-info"> <span> 7.1 years ago <a href="/u/11014/"> sandmann.t </a> ▴ 70 </span> </span> </div> <span class="diff-cont"></span> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </span> <div class="ui info message"> <p><a class="ui small label" href="/accounts/login/"> <i class="sign in icon"></i>Login</a> before adding your answer.</p> </div> <script> $(document).ready(function () { $('#subscribe').dropdown(); drag_and_drop(); $('.ui.dropdown').dropdown(); //var users = "**MISSING**".split(','); autocomplete_users(); //init_pagedown(); $(this).on('click', '#inplace .save', function () { event.preventDefault(); var post = $(this).closest('.post'); edit_dropdown_post(post); }); $(this).on('click', '#inplace .create', function () { event.preventDefault(); create_comment(); }); $(this).on('click', '.edit-button', function (event) { event.preventDefault(); inplace_form($(this)); }); $(this).on('click', ".add-comment", function () { inplace_form($(this), true); }); }); </script> </div> <div class="four wide column sidefeed"> <div class="ui large wrap-text" id="sidebar"> <div class="ui large wrap-text" id="sidebar"> <div class="title">Similar Posts</div> <div class="ui basic segment similar" id="similar"> <div id="similar-feed" post_uid="80845"></div> <div class="ui inverted dimmer"> <div class="content"> <div class="ui text loader"> <div class="muted">Loading Similar Posts</div> </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 434 users visited in the last hour</div> </div> <div class="ui three center aligned column stackable tiny grid"> <div class=" left aligned column" style="padding-right: 13%"> <b>Content</b> <a href="/#search-anchor">Search</a><br> <a href="/user/list/">Users</a><br> <a href="/t/">Tags</a><br> <a href="/b/list/">Badges</a> </div> <div class="left aligned column" style="padding-right: 12%"> <b>Help</b> <a href="/info/about/">About</a><br> <a href="/info/faq/">FAQ</a><br> </div> <div class=" left aligned column"> <b>Access</b> <a href="/info/rss/">RSS</a><br> <a href="/info/api/">API</a><br> <a href="#">Stats</a> </div> </div> <div class="ui divider"></div> <div class="ui vertical center aligned basic segment"> <p>Use of this site constitutes acceptance of our <a href="/info/policy/">User Agreement and Privacy Policy</a>.</p> <div class="smaller muted"> Powered by the <a href="https://github.com/ialbert/biostar-central" class="ui image"> <img src="/static/images/badge-forum.svg"></a> version 2.3.6 </div> </div> </div> </body> </html>